Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

Motivation: Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome.

Results: We introduce a novel pairwise structure alignment tool (rcsb.

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins.

Recent advances in Artificial Intelligence and Machine Learning (., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information.

Reproducible Speech Research With the Artificial Intelligence-Ready PERCEPT Corpora.

Background: Publicly available speech corpora facilitate reproducible research by providing open-access data for participants who have consented/assented to data sharing among different research teams. Such corpora can also support clinical education, including perceptual training and training in the use of speech analysis tools.

Purpose: In this research note, we introduce the PERCEPT (Perceptual Error Rating for the Clinical Evaluation of Phonetic Targets) corpora, PERCEPT-R (Rhotics) and PERCEPT-GFTA (Goldman-Fristoe Test of Articulation), which together contain over 36 hr of speech audio (> 125,000 syllable, word, and phrase utterances) from children, adolescents, and young adults aged 6-24 years with speech sound disorder (primarily residual speech sound disorders impacting /ɹ/) and age-matched peers.

Endothelial PHACTR1 Promotes Endothelial Activation and Atherosclerosis by Repressing PPARγ Activity Under Disturbed Flow in Mice.

Background: Numerous genome-wide association studies revealed that SNPs (single nucleotide polymorphisms) at the (phosphatase and actin regulator 1) locus strongly correlate with coronary artery disease. However, the biological function of PHACTR1 remains poorly understood. Here, we identified the proatherosclerotic effect of endothelial PHACTR1, contrary to macrophage PHACTR1.

RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides open access to experimentally-determined three-dimensional (3D) structures of biomolecules. The RCSB PDB RCSB.org research-focused web portal is used annually by many millions of users around the world.

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents.

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB.

Exploring word production in three-year-old monolingual French-speaking children.

There is a general need for more knowledge on the development of French phonology, and little information is currently available for typically developing French-speaking three-year-old children. This study took place in Belgium and explores the accuracy of speech production of 34 typically developing French-speaking children using a picture naming task. Measures of speech accuracy revealed lower performance than previously seen in the literature.

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies.

Motivation: Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level.

Results: We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

Availability And Implementation: https://github.

The development of preverbs in Northern East Cree: A longitudinal case study.

This study is based on naturalistic speech samples produced by one child learning Cree as her first language (2;01-4;03) and presents the first investigation into the development of preverbs in the language. Preverbs are an optional class of morpheme which precede the lexical verb stem, dividing into grammatical, lexical and directional (deictic) subclasses. Of nine preverb types in the child's inventory, 47/48 tokens are grammatical.

Simplified quality assessment for small-molecule ligands in the Protein Data Bank.

More than 70% of the experimentally determined macromolecular structures in the Protein Data Bank (PDB) contain small-molecule ligands. Quality indicators of ∼643,000 ligands present in ∼106,000 PDB X-ray crystal structures have been analyzed. Ligand quality varies greatly with regard to goodness of fit between ligand structure and experimental data, deviations in bond lengths and angles from known chemical structures, and inappropriate interatomic clashes between the ligand and its surroundings.

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.

Motivation: Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task.

Reduced Notch1 Cleavage Promotes the Development of Pulmonary Hypertension.

Clinical trials of Dll4 (Delta-like 4) neutralizing antibodies (Dll4nAbs) in cancer patients are ongoing. Surprisingly, pulmonary hypertension (PH) occurs in 14% to 18% of patients treated with Dll4nAbs, but the mechanisms have not been studied. Here, PH progression was measured in mice treated with Dll4nAbs.

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper.

Language and Learner Specific Influences on the Emergence of Consonantal Place and Manner Features.

This article focuses on the emergence of consonantal place and manner feature categories in the speech of first language learners. Starting with an overview of current representational approaches to phonology, we take the position that only models that allow for the emergence of phonological categories at all levels of phonological representation (from sub-segmental properties of speech sounds all the way to word forms represented within the child's lexicon) can account for the data. We begin with a cross-linguistic survey of the acquisition of rhotic consonants.

Automated phonological analysis and treatment target selection using AutoPATT.

Automated analyses of speech samples can offer improved accuracy and timesaving advantages that streamline clinical assessment for children with a suspected speech sound disorder. In this paper, we introduce AutoPATT, an automated tool for clinical analysis of speech samples. This free, open-source tool was developed as a plug-in for Phon and follows the procedures of the Phonological Analysis and Treatment Target Selection protocol, including extraction of a phonetic inventory, phonemic inventory with corresponding minimal pairs, and initial consonant cluster inventory.

Markedness and implicational relationships in phonological development: A cross-linguistic investigation.

Purpose: The complexity approach to speech disorders, based on the theoretical notion of phonological markedness, has been gaining interest over the last decade. In a nutshell, this approach suggests that the acquisition of phonologically marked units (e.g.

RCSB Protein Data Bank 1D tools and services.

Motivation: Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function.

Results: Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.

There is no phonology without abstract categories: A commentary on.

Ambridge's proposal cannot account for the most basic observations about phonological patterns in human languages. Outside of the earliest stages of phonological production by toddlers, the phonological systems of speakers/learners exhibit internal behaviours that point to the representation and processing of inter-related units ranging in size from sub-segmental (featural) and segmental to larger prosodic units ranging from the syllable all the way to the phonological utterance. Only theories which embrace these units can make proper predictions about phonological behaviours.

Isolation and Whole-Genome Sequencing of 12 Mushroom-Associated Bacterial Strains: an Inquiry-Based Laboratory Exercise in a Genomics Course at the Rochester Institute of Technology.

Here, we report the isolation, identification, and whole-genome sequences of 12 bacterial strains associated with four mushroom species. The study was done as an inquiry-based exercise in an undergraduate genomics course (BIOL 340) in the Thomas H. Gosnell School of Life Sciences at the Rochester Institute of Technology.